You may want to have the runout checked on both ends of the crank. My bike has a noticeable vibration so I asked to have the runout checked this time while they have it apart to fix the head gasket leak (for the third time). The camshaft/pinion end of the crank had .009" of runout -not enough to qualify for a crank/engine replacement, but still not good in my opinion. Next the dealer checked the runout on the drive/primary end of the crank and found .020" of runout using the procedures found in the bulletin d00d mentioned. That's enough to qualify for a new crankshaft at least...
I'm not sure why the Moco isn't warrantying the whole engine though. So far they have done the following repairs:
1. Replaced both head gaskets at approx. 7400 miles.
2. Replaced both cylinders, rings, and head gaskets at approx. 8500 miles.
3. Currently they are in the process of replacing both cylinders (again), rings, crankshaft, and head gaskets at approx. 10,000 miles.
My local dealer refused to check the crank runout even though I offered to pay for the procedure

so I took the bike to a dealer about 250 miles away. Then the local dealer called up and said they were ready to check the crank runout for me... Arrrrggghhh!!

My local dealer could never verify the vibration either, but the "other" dealer took it for a short ride and agreed that it DID have a vibration.
I'm not taking any chances on still having a vibration when I get the bike back so I have asked to have the reciprocating assembly (crank, rods, pistons) balanced before they put it back together with the new crank. Also asked them to check the runout on the new crank in a truing stand before doing anything. (They agreed and had already planned to check the new crank before using it.)
Good luck with your bike!